Research workbench
Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)- butyric acid complex
Analyse Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)- butyric acid complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZD3
- Type
- protein
- Length
- 547 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxide hydrolase 2, cytoplasmic
- EC
- 3.3.2.3
- UniProt
- P34913
- Ligands
- NC4, MG, PO4
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxide hydrolase 2, cytoplasmic (EC 3.3.2.3) | protein | 547 | 46% helix, 14% strand | P34913 |
Ligands and binding sites
- NC4 · 4-{[(cyclohexylamino)carbonyl]amino}butanoic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- 15P · Polyethylene glycol (N=34) · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.84 | 0.88 | 57 | NC4 |
| 2 | 241 | 0.66 | 0.83 | 32 | MG, PO4 |
| 3 | 384 | 0.58 | 0.75 | 28 | empty |
Compared structures
- 1ZD3 · Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-butyric acid complex · the same entry in another collection · chain A against A, TM-score 1.00
- P34913 · AlphaFold monomer V2.0 prediction for bifunctional epoxide hydrolase 2 (P34913) · a predicted model of the same protein · chain A against A, TM-score 0.72
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P34913
- Elsewhere: RCSB PDB 1ZD3 · PDBe 1ZD3 · UniProt P34913
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